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Commit 3e21675

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author
schutzekatze
committed
Update btllib in RResolver
1 parent 027f3fa commit 3e21675

31 files changed

Lines changed: 923 additions & 3948 deletions

RResolver/btllib/extras/java/BloomFilter.java

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -101,11 +101,11 @@ public String get_hash_fn() {
101101
}
102102

103103
public void save(String path) {
104-
btllibJNI.BloomFilter_save(swigCPtr, this, path);
104+
btllibJNI.BloomFilter_save__SWIG_0(swigCPtr, this, path);
105105
}
106106

107-
public static SWIGTYPE_p_std__shared_ptrT_cpptoml__table_t parse_header(SWIGTYPE_p_std__ifstream file, String magic_string) {
108-
return new SWIGTYPE_p_std__shared_ptrT_cpptoml__table_t(btllibJNI.BloomFilter_parse_header(SWIGTYPE_p_std__ifstream.getCPtr(file), magic_string), true);
107+
public static void save(String path, SWIGTYPE_p_cpptoml__table table, String data, long n) {
108+
btllibJNI.BloomFilter_save__SWIG_1(path, SWIGTYPE_p_cpptoml__table.getCPtr(table), data, n);
109109
}
110110

111111
}

RResolver/btllib/extras/java/DataSink.java

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -8,11 +8,12 @@
88

99
package btllib;
1010

11-
public class DataSink extends DataStream {
11+
public class DataSink {
1212
private transient long swigCPtr;
13+
protected transient boolean swigCMemOwn;
1314

1415
protected DataSink(long cPtr, boolean cMemoryOwn) {
15-
super(btllibJNI.DataSink_SWIGUpcast(cPtr), cMemoryOwn);
16+
swigCMemOwn = cMemoryOwn;
1617
swigCPtr = cPtr;
1718
}
1819

@@ -33,7 +34,6 @@ public synchronized void delete() {
3334
}
3435
swigCPtr = 0;
3536
}
36-
super.delete();
3737
}
3838

3939
public DataSink(String path, boolean append) {

RResolver/btllib/extras/java/DataSource.java

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -8,11 +8,12 @@
88

99
package btllib;
1010

11-
public class DataSource extends DataStream {
11+
public class DataSource {
1212
private transient long swigCPtr;
13+
protected transient boolean swigCMemOwn;
1314

1415
protected DataSource(long cPtr, boolean cMemoryOwn) {
15-
super(btllibJNI.DataSource_SWIGUpcast(cPtr), cMemoryOwn);
16+
swigCMemOwn = cMemoryOwn;
1617
swigCPtr = cPtr;
1718
}
1819

@@ -33,7 +34,6 @@ public synchronized void delete() {
3334
}
3435
swigCPtr = 0;
3536
}
36-
super.delete();
3737
}
3838

3939
public DataSource(String path) {

RResolver/btllib/extras/java/DataStream.java

Lines changed: 0 additions & 103 deletions
This file was deleted.

RResolver/btllib/extras/java/ProcessPipelineInternal.java

Lines changed: 0 additions & 47 deletions
This file was deleted.

RResolver/btllib/extras/java/SWIGTYPE_p_FILE.java renamed to RResolver/btllib/extras/java/SWIGTYPE_p_cpptoml__table.java

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -8,18 +8,18 @@
88

99
package btllib;
1010

11-
public class SWIGTYPE_p_FILE {
11+
public class SWIGTYPE_p_cpptoml__table {
1212
private transient long swigCPtr;
1313

14-
protected SWIGTYPE_p_FILE(long cPtr, @SuppressWarnings("unused") boolean futureUse) {
14+
protected SWIGTYPE_p_cpptoml__table(long cPtr, @SuppressWarnings("unused") boolean futureUse) {
1515
swigCPtr = cPtr;
1616
}
1717

18-
protected SWIGTYPE_p_FILE() {
18+
protected SWIGTYPE_p_cpptoml__table() {
1919
swigCPtr = 0;
2020
}
2121

22-
protected static long getCPtr(SWIGTYPE_p_FILE obj) {
22+
protected static long getCPtr(SWIGTYPE_p_cpptoml__table obj) {
2323
return (obj == null) ? 0 : obj.swigCPtr;
2424
}
2525
}

RResolver/btllib/extras/java/SWIGTYPE_p_std__ifstream.java

Lines changed: 0 additions & 26 deletions
This file was deleted.

RResolver/btllib/extras/java/SWIGTYPE_p_std__shared_ptrT_cpptoml__table_t.java

Lines changed: 0 additions & 26 deletions
This file was deleted.

RResolver/btllib/extras/java/SeedBloomFilter.java

Lines changed: 6 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -108,8 +108,8 @@ public double get_occupancy() {
108108
return btllibJNI.SeedBloomFilter_get_occupancy(swigCPtr, this);
109109
}
110110

111-
public long get_hash_num() {
112-
return btllibJNI.SeedBloomFilter_get_hash_num(swigCPtr, this);
111+
public long get_total_hash_num() {
112+
return btllibJNI.SeedBloomFilter_get_total_hash_num(swigCPtr, this);
113113
}
114114

115115
public double get_fpr() {
@@ -132,6 +132,10 @@ public long get_hash_num_per_seed() {
132132
return btllibJNI.SeedBloomFilter_get_hash_num_per_seed(swigCPtr, this);
133133
}
134134

135+
public long get_hash_num() {
136+
return btllibJNI.SeedBloomFilter_get_hash_num(swigCPtr, this);
137+
}
138+
135139
public String get_hash_fn() {
136140
return btllibJNI.SeedBloomFilter_get_hash_fn(swigCPtr, this);
137141
}

RResolver/btllib/extras/java/SeqReaderFastaModule.java

Lines changed: 0 additions & 43 deletions
This file was deleted.

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